Although the cure rate for T cell Acute Lymphoblastic Leukemia (T-ALL) has been improved dramatically during the last couple of decades, the overall prognosis remains dismal, due to frequent disease relapse and the absence of non-cytotoxic targeted therapy options. The role of epigenetic regulation in T-ALL initiation and progression has recently been addressed. Despite the fact that drugs targeting the function of key epigenetic factors, such as histone deacetylase (HDAC) and DNA methyltransferase (DNMT) (Baylin & Jones, “A Decade of Exploring the Cancer Epigenome: Biological and Translational Implications,” Nature Rev. Cancer 11:726-734 (2011); Boumber & Issa, “Epigenetics in Cancer: What's the Future?” Oncology 25:220-226, 228 (2011)), have been approved in the context of hematopoietic disorders, “epigenetic” drugs are currently not used for T-ALL treatment. The recent identification of mutations affecting chromatin modulators in a variety of leukemias (Zhang et al., “The Genetic Basis of Early T-Cell Precursor Acute Lymphoblastic Leukaemia,” Nature 481:157-163 (2012); Holmfeldt et al., “The Genomic Landscape of Hypodiploid Acute Lymphoblastic Leukemia,” Nature Genetics 45:242-252 (2013); Roberts & Mullighan, “How New Advances in Genetic Analysis are Influencing the Understanding and Treatment of Childhood Acute Leukemia,” Curr. Opin. Pediatr. 23:34-40 (2011); Shih et al., “The Role of Mutations in Epigenetic Regulators in Myeloid Malignancies,” Nat. Rev. Cancer 12:599-612 (2012); Jankowska et al., “Mutational Spectrum Analysis of Chronic Myelomonocytic Leukemia Includes Genes Associated With Epigenetic Regulation: UTX, EZH2, and DNMT3A.” Blood 118:3932-3941(2011); Ntziachristos et al., “Mechanisms of Epigenetic Regulation of Leukemia Onset and Progression,” Adv. Immunol. 117:1-38 (2013)) along with a plethora of recently generated animal models of disease have shed light on the mechanisms of action for this class of epigenetic modifiers in blood cancers. Nevertheless, there is an unmet need for development and utilization of drugs that target the epigenome (McCabe et al., “EZH2 Inhibition as a Therapeutic Strategy for Lymphoma with EZH2-Activating Mutations,” Nature 492:108-112 (2012); Kruidenier et al., “A Selective Jumonji H3K27 Demethylase Inhibitor Modulates the Proinflammatory Macrophage Response,” Nature 488:404-408 (2012); Filippakopoulos et al., “Selective Inhibition of BET Bromodomains,” Nature 468:1067-1073 (2010); Delmore et al., “BET Bromodomain Inhibition as a Therapeutic Strategy to Target c-Myc,” Cell 146:904-917 (2011); Bernt et al., “MLL-Rearranged Leukemia is Dependent on Aberrant H3K79 Methylation by DOT1L,” Cancer Cell 20:66-78 (2011)) in pediatric acute leukemia.
There are currently two characterized H3K27 demethylases that belong to the Jumonji family of deoxygenases. UTX (Hubner & Spector, “Role of H3K27 Demethylases Jmjd3 and UTX in Transcriptional Regulation,” Cold Spring Harb. Symp. Quant. Biol. 75:43-49 (2011); Kooistra & Helin, “Molecular Mechanisms and Potential Functions of Histone Demethylases,” Nature Rev. Mol. Cell Biol. 13:297-311(2012)) (KDM6A) is a ubiquitously expressed protein that controls basal levels of H3K27me3, whereas JMJD3(KDM6B) is induced upon inflammation (De Santa et al., “The Histone H3 Lysine-27 DemethylaseJmjd3 Links Inflammation to Inhibition of Polycomb-Mediated Gene Silencing,” Cell 130:1083-1094 (2007)), viral, and oncogenic stimuli (Anderton et al., “The H3K27me3 Demethylase, KDM6B, is Induced by Epstein-Barr Virus and Over-Expressed in Hodgkin's Lymphoma.” Oncogene 30:2037-2043 (2011); Agger et al., “The H3K27me3 Demethylase JMJD3 Contributes to the Activation of the INK4AARF Locus in Response to Oncogene- and Stress-Induced Senescence,” Genes Dev. 23:1171-1176 (2009); Barradas et al., “Histone Demethylase JMJD3 Contributes to Epigenetic Control of INK4a/ARF by Oncogenic RAS,” Genes Dev. 23:1177-1182 (2009)). JMJD3 is important for neuronal differentiation (Jepsen et al., “SMRT-Mediated Repression of an H3K27 Demethylase in Progression from Neural Stem Cell to Neuron,” Nature 450:415-419 (2007)) and promotes epidermal cell differentiation (Sen et al., “Control of Differentiation in a Self-Renewing Mammalian Tissue by the Histone Demethylase JMJD3,” Genes Dev. 22:1865-1870 (2008)). UTX, in turn, is important for induction of ectoderm and mesoderm differentiation (Morales et al., “Utx Is Required for Proper Induction of Ectoderm and Mesoderm During Differentiation of Embryonic Stem Cells,” PLoS One 8:e60020 (2013); Wang et al., “UTX Regulates Mesoderm Differentiation of Embryonic Stem Cells Independent of H3K27 Demethylase Activity,” Proc. Natl. Acad. Sci. USA 109:15324-15329 (2012)). Both have been shown to promote differentiation through expression of the HOX genes (Agger et al., “UTX and JMJD3 are Histone H3K27 Demethylases Involved in HOX Gene Regulation and Development,” Nature 449:731-734 (2007); Lee et al., “Demethylation of H3K27 Regulates Polycomb Recruitment and H2A Ubiquitination,” Science 318:447-450 (2007)). Interestingly, JMJD3 and UTX have been found to play different roles in embryonic stem cell physiology, where JMJD3 has been found to inhibit reprogramming with its dual function on INK4a/Arf expression and by mediating PHF20 ubiquitination (Zhao et al., “Jmjd3 Inhibits Reprogramming by Upregulating Expression of INK4a/Arf and Targeting PHF20 for Ubiquitination,” Cell 152:1037-1050 (2013)), whereas UTX seems to be essential for reprogramming (Mansour et al., “The H3K27 Demethylase Utx Regulates Somatic and Germ Cell Epigenetic Reprogramming,” Nature 488:409-413 (2012)). Despite such compelling results in developmental systems, the overall understanding of H3K27 demethylases in cancer remains extremely limited (Agger et al., “The H3K27me3 Demethylase JMJD3 Contributes to the Activation of the INK4AARF Locus in Response to Oncogene- and Stress-Induced Senescence,” Genes Dev. 23:1171-1176 (2009); Barradas et al., “Histone Demethylase JMJD3 Contributes to Epigenetic Control of INK4a/ARF by Oncogenic RAS,” Genes Dev. 23:1177-1182 (2009)). UTX has been found to control cell fate (Wang et al., “The Histone Demethylase UTX Enables RB-Dependent Cell Fate Control,” Genes Dev. 24:327-332 (2010)) and to be implicated mainly in solid tumors and less in hematological malignancies (Wang et al., “The Histone Demethylase UTX Enables RB-Dependent Cell Fate Control,” Genes Dev. 24:327-332 (2010); Tsai et al., “Tumor Suppression by the Histone Demethylase UTX,” Cell Cycle 9:2043-2044 (2010); Liu et al., “A Functional Role for the Histone Demethylase UTX in Normal and Malignant Hematopoietic Cells,” Exp. Hematol. 40:487-498 e483 (2012); Thieme et al., “The Histone Demethylase UTX Regulates Stem Cell Migration and Hematopoiesis,” Blood 121:2462-2473 (2013)), a finding supported mainly through the identification of inactivating mutations (Jankowska et al., “Mutational Spectrum Analysis of Chronic Myelomonocytic Leukemia Includes Genes Associated With Epigenetic Regulation: UTX, EZH2, and DNMT3A.” Blood 118:3932-3941(2011); Thieme et al., “The Histone Demethylase UTX Regulates Stem Cell Migration and Hematopoiesis,” Blood 121:2462-2473 (2013); van Haaften et al., “Somatic Mutations of the Histone H3K27 Demethylase Gene UTX in Human Cancer,” Nature Genet. 41:521-523 (2009); Mar et al., “Sequencing Histone-Modifying Enzymes Identifies UTX Mutations in Acute Lymphoblastic Leukemia,” Leukemia 26:1881-1883 (2012)). However, the roles of these two demethylases as direct modulators of the oncogenic state are largely uncharacterized.
The present invention is directed to overcoming these and other deficiencies in the art.